If a bit of time took place between the alliance with the Shivans, and the declaration of the HoL revival and the beginning of hostilities, it might allow time for the collaboration between the two sides in terms of technology. If you chose to get someone to make some MODs for you, you could have Vasudan style fighters, with Shivan design elements and enhanced specs. This could be done with a partial reskin, but a new design would look better. You could even add later episode around a new V-S destroyer and/or cruiser design, as shades of Silent Threat and the Hades. To add an even greater plot twist, you could even re-introduce those escaped elements of the NTF... Bosch included. They could either be assigned by the Shivans to facilitate their introduction into the HoL and add some strategic cunning of their own, or perhaps with the HoL in posession of ETAK, they could communicate with the Shivans and possibly convince them to abandon their allience with Bosch and the NTF. This could lead to Bosch fleeing the Shivans, with whatever advanced technology and ships he could steal, and returning to Polaris or possibly Sol in an attempt to gain control of the military and possibly the allied goverment. His plan might be to assume control of the Terran half of the GTVA (one way or another) and using the advanced Shivan technology he stole, beef up the Terran fleet and take revenge on the HoL, the Shivans, or possibly even the Vasudans as a whole. We all had this notion that Bosch intended to one day return to the GTVA with the Shivans following him, and assume power... kind of like Baltar from Battlestar Gallactica. As such, the idea of him wanting to retake control of the GTVA (or GTA if he plans on edging out the Vasudans) isn't all that far fetched in my mind.
That was probably
more involved than you were planning on... in fact it was more involved than I was thinking when I first started this post. Oh well... I hope it gives you ideas... and if their good ideas, even better!